Following the February 2007 incident in which the airline was forced to cancel nearly 1,700 flights due to winter storms, jetBlue's board of directors replaced founder and Chief Executive Officer David Neeleman with Dave Barger.[21] He had politicked the board, while Neeleman was busy publicly apologizing. Barger's ascendancy caused widespread demoralization in the ranks.[22] He became JetBlue's new Chief Executive Officer on May 10, 2007.[23] Neeleman, the company's founder and largest individual investor, became a nonexecutive chairman as a result of the change.[24]
In December 2015, the FAA issued a letter of correction due to an incident where an Allegiant aircraft attempted to fly to Hector International Airport in Fargo, ND in late July 2015, which was at the time within a temporary flight restriction due to a rehearsal by the Blue Angels flight team for an upcoming air show in Fargo respectively.[60] The pilots flying the aircraft then declared a fuel emergency stating, "Yeah, listen, we're bingo (empty) fuel here in about probably three to four minutes and I got to come in and land." The pilots were scolded by the airport's tower who said, "Your company … should have been aware of this for a number of months," regarding the airspace restrictions which would have prevented flight to the airport. The pilots flying the aircraft were, at the time, the airline's vice president of flight operations and its director of flight safety.[61]
On September 9, 2014, Frontier introduced an updated livery,[86] as part of a rebranding that saw the spokesanimals' roles increase. The new livery reintroduced a green "FRONTIER" typeface to the fuselage, featuring the stylized "F" designed by Saul Bass for the original Frontier in 1978. Each aircraft features the name of the animal featured on its tail near the nose of the aircraft for easier identification. Currently about twenty five aircraft in the Frontier fleet feature the new livery.

A new marketing strategy has been partnerships with professional sports teams and venues. As the official airline of the New York Jets, JetBlue has specially painted the exterior of one of their Airbus A320s (N746JB) in the team's colors. Aircraft N605JB is based on the design of the Boston Red Sox road uniform and sports a grey fuselage with navy lettering. This aircraft was unveiled in February 2012, just in time for the opening of the Red Sox new spring training facility in Fort Myers, Florida named JetBlue Park at Fenway South. Additionally, JetBlue and MasterCard have pledged to refund select flight purchases made online at JetBlue.com using a MasterCard.[96] JetBlue has also partnered with various other sports teams and sporting venues in cities they serve.